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Conference Paper

The Montagues and the Capulets Carole Goble* and Chris Wroe The School of Computer Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK *Correspondence to: Carole Goble, The School of Computer Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK. E-mail: carole.goble/[email protected] manchester.ac.uk

Received: 11 November 2004 Revised: 15 November 2004 Accepted: 16 November 2004

Abstract Prologue Two households, both alike in dignity, In fair Genomics, where we lay our scene, (One, comforted by its logic’s rigour, Claims ontology for the realm of pure, The other, with blessed scientist’s vigour, Acts hastily on models that endure), From ancient grudge break to new mutiny, When ‘being’ drives a fly-man to blaspheme. From forth the fatal loins of these two foes, Researchers to unlock the book of life; Whole misadventured piteous overthrows, Can with their work bury their clans’ strife. The fruitful passage of their GO-mark’d love, And the continuance of their studies sage, Which, united, yield ontologies undreamed-of, Is now the hour’s traffic of our stage; The which if you with patient ears attend, What here shall miss, our toil shall strive to mend. Copyright  2005 John Wiley & Sons, Ltd.

Stage notes 1. This paper is a write-up of the opening plenary talk of the SOFG2 conference (http://www.sofg. org/meetings). Delegates throughout the rest of the meeting named themselves as Montagues and Capulets — which was revealing in itself. 2. For the sake of effect, we make sweeping generalizations.

We lay our scene In recent years, ontologies have taken centre stage as their importance within life sciences grows. Interoperating resources, intelligent mining and sharing knowledge, be it by people or computer systems, requires a consistent shared understanding of what the information means. The life science community have an immediate and pressing need for controlled vocabularies if they are to successfully glue together and classify the numerous results populating their expanding collection of data resources. As a measure of the interest in the topic, over 700 people attended the opening paper of the ontology track at ISMB 2004 in Glasgow Copyright  2005 John Wiley & Sons, Ltd.

(Joslyn et al., 2004) and over 60 were locked out of the room demanding entry. The effective development of large ontologies, and their wide deployment, requires appropriate languages and mechanisms. We need languages that permit the formal and explicit specification of the meaning of terms, so that these meanings are machine-interpretable, can be unambiguously shared and can be used to computationally infer new knowledge. We also need mechanisms for ontology development, deployment and maintenance. Conveniently, the Computer Science/Artificial Intelligence communities work on knowledge representation techniques and technologies that should benefit the Life Scientist. Life Scientists, in turn, supply the Computer Scientists with practical, realistic problems as an ideal source of requirements, and provide a community of early adopters to pilot their solutions. However, despite the obvious mutual benefit, the two communities often find themselves in conflict, mostly due to misunderstandings of the motivations that lie behind the communities, a lack of awareness of the aspects of their own characters that frustrate the other and, perhaps, a failure to recognize that collaboration will mean compromise. It was ever thus. We have

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a roadmap to chart the rivalry and reconciliations between these two Houses (Shakespeare, 1596). We follow this to make explicit the characters of these two Houses (or three as it turns out), highlight some of the reasons for their quarrels, and identify opportunities for reconciliation that we hope will lead to a happy outcome, rather than a tragedy.

The Houses of Genomics Bioinformatics is already an interdisciplinary topic encompassing the many disciplines of the ‘omics’ — genomics, proteomics, metabolomics, transcriptomics — together with chemoinformatics, medical informatics, phenotypical observation, phylogeny, anatomy and so on. This mixing of disciplines is itself a challenge and, added to that, is the challenge of underpinning the bioinformatics by introducing Computer Scientists. In addition, the fields of ontology and knowledge management have their own communities. Thus, in fair Genomics, where we lay our scene there are a number of Houses. In fact there are three, rather than the traditional two — Computer Scientists, Life Scientists and Philosophers.

The Montagues One, comforted by its logic’s rigour/Claims ontology for the realm of pure. This is the House of Computer Science, knowledge management and artificial intelligence (AI). Their interests lay in the logics and languages needed for the organization and representation of ontologies and knowledge bases that can support intelligent reasoning and logical inference. Theory is their strong point, with a traditional desire for orderliness, consistency, coherency and proof. They like their knowledge to be we